Job ID = 6983660 sra ファイルのダウンロード中... Completed: 351226K bytes transferred in 6 seconds (414739K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 101 2547 0 2547 0 0 3681 0 --:--:-- --:--:-- --:--:-- 4945 100 36072 0 36072 0 0 41559 0 --:--:-- --:--:-- --:--:-- 52202 sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 15060643 spots for /home/okishinya/chipatlas/results/dm3/SRX017470/SRR037527.sra Written 15060643 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:03 15060643 reads; of these: 15060643 (100.00%) were unpaired; of these: 539863 (3.58%) aligned 0 times 10186320 (67.64%) aligned exactly 1 time 4334460 (28.78%) aligned >1 times 96.42% overall alignment rate Time searching: 00:05:03 Overall time: 00:05:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2863362 / 14520780 = 0.1972 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sun, 05 Jun 2016 15:42:53: # Command line: callpeak -t SRX017470.bam -f BAM -g dm -n SRX017470.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX017470.05 # format = BAM # ChIP-seq file = ['SRX017470.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Sun, 05 Jun 2016 15:42:53: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:42:53: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:42:53: # Command line: callpeak -t SRX017470.bam -f BAM -g dm -n SRX017470.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX017470.10 # format = BAM # ChIP-seq file = ['SRX017470.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Sun, 05 Jun 2016 15:42:53: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:42:53: # Command line: callpeak -t SRX017470.bam -f BAM -g dm -n SRX017470.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX017470.20 # format = BAM # ChIP-seq file = ['SRX017470.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off INFO @ Sun, 05 Jun 2016 15:42:53: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:42:53: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:42:53: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:42:57: 1000000 INFO @ Sun, 05 Jun 2016 15:42:57: 1000000 INFO @ Sun, 05 Jun 2016 15:42:58: 1000000 INFO @ Sun, 05 Jun 2016 15:43:02: 2000000 INFO @ Sun, 05 Jun 2016 15:43:02: 2000000 INFO @ Sun, 05 Jun 2016 15:43:03: 2000000 INFO @ Sun, 05 Jun 2016 15:43:07: 3000000 INFO @ Sun, 05 Jun 2016 15:43:07: 3000000 INFO @ Sun, 05 Jun 2016 15:43:08: 3000000 INFO @ Sun, 05 Jun 2016 15:43:11: 4000000 INFO @ Sun, 05 Jun 2016 15:43:12: 4000000 INFO @ Sun, 05 Jun 2016 15:43:13: 4000000 INFO @ Sun, 05 Jun 2016 15:43:16: 5000000 INFO @ Sun, 05 Jun 2016 15:43:17: 5000000 INFO @ Sun, 05 Jun 2016 15:43:18: 5000000 INFO @ Sun, 05 Jun 2016 15:43:21: 6000000 INFO @ Sun, 05 Jun 2016 15:43:22: 6000000 INFO @ Sun, 05 Jun 2016 15:43:23: 6000000 INFO @ Sun, 05 Jun 2016 15:43:25: 7000000 INFO @ Sun, 05 Jun 2016 15:43:27: 7000000 INFO @ Sun, 05 Jun 2016 15:43:29: 7000000 INFO @ Sun, 05 Jun 2016 15:43:30: 8000000 INFO @ Sun, 05 Jun 2016 15:43:32: 8000000 INFO @ Sun, 05 Jun 2016 15:43:34: 8000000 INFO @ Sun, 05 Jun 2016 15:43:35: 9000000 INFO @ Sun, 05 Jun 2016 15:43:37: 9000000 INFO @ Sun, 05 Jun 2016 15:43:39: 9000000 INFO @ Sun, 05 Jun 2016 15:43:40: 10000000 INFO @ Sun, 05 Jun 2016 15:43:41: 10000000 INFO @ Sun, 05 Jun 2016 15:43:44: 10000000 INFO @ Sun, 05 Jun 2016 15:43:45: 11000000 INFO @ Sun, 05 Jun 2016 15:43:46: 11000000 INFO @ Sun, 05 Jun 2016 15:43:48: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:43:48: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:43:48: #1 total tags in treatment: 11657418 INFO @ Sun, 05 Jun 2016 15:43:48: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:43:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:43:49: 11000000 INFO @ Sun, 05 Jun 2016 15:43:49: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:43:49: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:43:49: #1 total tags in treatment: 11657418 INFO @ Sun, 05 Jun 2016 15:43:49: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:43:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:43:50: #1 tags after filtering in treatment: 11656705 INFO @ Sun, 05 Jun 2016 15:43:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:43:50: #1 finished! INFO @ Sun, 05 Jun 2016 15:43:50: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:43:51: #1 tags after filtering in treatment: 11656705 INFO @ Sun, 05 Jun 2016 15:43:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:43:51: #1 finished! INFO @ Sun, 05 Jun 2016 15:43:51: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:43:53: #2 number of paired peaks: 437 WARNING @ Sun, 05 Jun 2016 15:43:53: Fewer paired peaks (437) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 437 pairs to build model! INFO @ Sun, 05 Jun 2016 15:43:53: start model_add_line... INFO @ Sun, 05 Jun 2016 15:43:53: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:43:53: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:43:53: #1 total tags in treatment: 11657418 INFO @ Sun, 05 Jun 2016 15:43:53: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:43:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:43:54: #2 number of paired peaks: 437 WARNING @ Sun, 05 Jun 2016 15:43:54: Fewer paired peaks (437) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 437 pairs to build model! INFO @ Sun, 05 Jun 2016 15:43:54: start model_add_line... INFO @ Sun, 05 Jun 2016 15:43:55: #1 tags after filtering in treatment: 11656705 INFO @ Sun, 05 Jun 2016 15:43:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:43:55: #1 finished! INFO @ Sun, 05 Jun 2016 15:43:55: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:43:57: #2 number of paired peaks: 437 WARNING @ Sun, 05 Jun 2016 15:43:57: Fewer paired peaks (437) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 437 pairs to build model! INFO @ Sun, 05 Jun 2016 15:43:57: start model_add_line... INFO @ Sun, 05 Jun 2016 15:43:57: start X-correlation... INFO @ Sun, 05 Jun 2016 15:43:57: end of X-cor INFO @ Sun, 05 Jun 2016 15:43:57: #2 finished! INFO @ Sun, 05 Jun 2016 15:43:57: #2 predicted fragment length is 70 bps INFO @ Sun, 05 Jun 2016 15:43:57: #2 alternative fragment length(s) may be 3,70 bps INFO @ Sun, 05 Jun 2016 15:43:57: #2.2 Generate R script for model : SRX017470.20_model.r WARNING @ Sun, 05 Jun 2016 15:43:57: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:43:57: #2 You may need to consider one of the other alternative d(s): 3,70 WARNING @ Sun, 05 Jun 2016 15:43:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:43:57: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:43:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:43:58: start X-correlation... INFO @ Sun, 05 Jun 2016 15:43:58: end of X-cor INFO @ Sun, 05 Jun 2016 15:43:58: #2 finished! INFO @ Sun, 05 Jun 2016 15:43:58: #2 predicted fragment length is 70 bps INFO @ Sun, 05 Jun 2016 15:43:58: #2 alternative fragment length(s) may be 3,70 bps INFO @ Sun, 05 Jun 2016 15:43:58: #2.2 Generate R script for model : SRX017470.10_model.r WARNING @ Sun, 05 Jun 2016 15:43:58: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:43:58: #2 You may need to consider one of the other alternative d(s): 3,70 WARNING @ Sun, 05 Jun 2016 15:43:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:43:58: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:43:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:44:01: start X-correlation... INFO @ Sun, 05 Jun 2016 15:44:01: end of X-cor INFO @ Sun, 05 Jun 2016 15:44:01: #2 finished! INFO @ Sun, 05 Jun 2016 15:44:01: #2 predicted fragment length is 70 bps INFO @ Sun, 05 Jun 2016 15:44:01: #2 alternative fragment length(s) may be 3,70 bps INFO @ Sun, 05 Jun 2016 15:44:01: #2.2 Generate R script for model : SRX017470.05_model.r WARNING @ Sun, 05 Jun 2016 15:44:01: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:44:01: #2 You may need to consider one of the other alternative d(s): 3,70 WARNING @ Sun, 05 Jun 2016 15:44:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:44:01: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:44:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:44:58: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:45:00: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:45:06: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:45:43: #4 Write output xls file... SRX017470.20_peaks.xls INFO @ Sun, 05 Jun 2016 15:45:43: #4 Write peak in narrowPeak format file... SRX017470.20_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:45:43: #4 Write summits bed file... SRX017470.20_summits.bed INFO @ Sun, 05 Jun 2016 15:45:43: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (515 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 05 Jun 2016 15:45:48: #4 Write output xls file... SRX017470.10_peaks.xls INFO @ Sun, 05 Jun 2016 15:45:48: #4 Write peak in narrowPeak format file... SRX017470.10_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:45:48: #4 Write summits bed file... SRX017470.10_summits.bed INFO @ Sun, 05 Jun 2016 15:45:48: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1148 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 05 Jun 2016 15:45:53: #4 Write output xls file... SRX017470.05_peaks.xls INFO @ Sun, 05 Jun 2016 15:45:53: #4 Write peak in narrowPeak format file... SRX017470.05_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:45:53: #4 Write summits bed file... SRX017470.05_summits.bed INFO @ Sun, 05 Jun 2016 15:45:53: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1982 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。